Yes you and/or /u/72skidoo depending on whether you're different peeople posted before a bunch of times. Congratulations on deciphering it. But reading the literature on that MS (Schmeh, 2014) the encryption had been solved already by that date, and is apparently just a simple monoalphabetic substitution cipher. Figuring out the why and where and when is a lot more work, requires knowledge of Latin and Dutch and possibly other topics like paleography. Above all it requires access to the MS or at least a digitized version, which the BL doesn't have online and which you're not providing. Bottom line here is that you're asking for something that requires actual primary research here. It likely requires more effort - and definitely more knowledge- than the decipherment does.

In short, and to be honest, it sounds like you're reading much too much into the fact that it's enciphered. It was a common thing in the Renaissance, particularly after publications like Vigenère's Treaty on ciphers or secret means of writing (1586) and Johannes Trithemius' Steganographia (published 1606 but written a century earlier) Lots of people in the 1600s wrote diaries and letters and notebooks in codes they'd invented. (here's an MS of the era with 65 magical/cryptological alphabets)

So it was common and the fact that something is written with cipher does not mean the actual text contains anything deeply secret. In fact in most cases in that era it does not. Also, simple substitution ciphers were weak and known to be easily broken back then too and serious contexts (e.g. diplomatic correspondence) used more sophisticated ciphers.

In this case, I gather there apparently was the usual Latin scribal abbreviations in the ciphertext! Which immediately makes it obvious to the literate reader of the time, who is accustomed to such abbreviations, that the underlying language is Latin and that it's probably a monoalphabetic cipher.

"christus ex maria virgine natus est"

I fail to see how that's a message or a secret. (or proves it's not a hoax, although I see no particular reason to think it is) "Christ is born from the virgin Mary" is not a controversial statement to either a Catholic or Protestant and it is a stock phrase, occurring for instance in the medieval carol Gaudete.

Honestly, it's not necessarily anything more exciting than someone's Latin homework, written in code because writing personal notebooks in code was relatively popular at the time. Just staying with the British Library, Harley MS 7576 is from the 17th century and has some simple ciphertext in it and also some pages of Latin phrases and English. In this case the Latin phrases aren't enciphered but the point is that neither of these things are that uncommon.